{"id":"https://openalex.org/W4410372430","doi":"https://doi.org/10.1007/978-3-031-89704-7_24","title":"TARNAS, a\u00a0TrAnslator for\u00a0RNA Secondary Structure Formats","display_name":"TARNAS, a\u00a0TrAnslator for\u00a0RNA Secondary Structure Formats","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4410372430","doi":"https://doi.org/10.1007/978-3-031-89704-7_24"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-031-89704-7_24","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-89704-7_24","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-89704-7_24.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-89704-7_24.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030309728","display_name":"Michela Quadrini","orcid":"https://orcid.org/0000-0003-0539-0290"},"institutions":[{"id":"https://openalex.org/I112859197","display_name":"Universit\u00e0 di Camerino","ror":"https://ror.org/0005w8d69","country_code":"IT","type":"education","lineage":["https://openalex.org/I112859197"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Michela Quadrini","raw_affiliation_strings":["School of Sciences and Technology, University of Camerino, Camerino, MC, Italy"],"raw_orcid":"https://orcid.org/0000-0003-0539-0290","affiliations":[{"raw_affiliation_string":"School of Sciences and Technology, University of Camerino, Camerino, MC, Italy","institution_ids":["https://openalex.org/I112859197"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117544806","display_name":"Piero Hierro Canchari","orcid":null},"institutions":[{"id":"https://openalex.org/I112859197","display_name":"Universit\u00e0 di Camerino","ror":"https://ror.org/0005w8d69","country_code":"IT","type":"education","lineage":["https://openalex.org/I112859197"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Piero Hierro Canchari","raw_affiliation_strings":["School of Sciences and Technology, University of Camerino, Camerino, MC, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Sciences and Technology, University of Camerino, Camerino, MC, Italy","institution_ids":["https://openalex.org/I112859197"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117544807","display_name":"Piermichele Rosati","orcid":null},"institutions":[{"id":"https://openalex.org/I112859197","display_name":"Universit\u00e0 di Camerino","ror":"https://ror.org/0005w8d69","country_code":"IT","type":"education","lineage":["https://openalex.org/I112859197"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Piermichele Rosati","raw_affiliation_strings":["School of Sciences and Technology, University of Camerino, Camerino, MC, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Sciences and Technology, University of Camerino, Camerino, MC, Italy","institution_ids":["https://openalex.org/I112859197"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076735277","display_name":"Luca Tesei","orcid":"https://orcid.org/0000-0002-7536-8796"},"institutions":[{"id":"https://openalex.org/I112859197","display_name":"Universit\u00e0 di Camerino","ror":"https://ror.org/0005w8d69","country_code":"IT","type":"education","lineage":["https://openalex.org/I112859197"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luca Tesei","raw_affiliation_strings":["School of Sciences and Technology, University of Camerino, Camerino, MC, Italy"],"raw_orcid":"https://orcid.org/0000-0002-7536-8796","affiliations":[{"raw_affiliation_string":"School of Sciences and Technology, University of Camerino, Camerino, MC, Italy","institution_ids":["https://openalex.org/I112859197"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5030309728"],"corresponding_institution_ids":["https://openalex.org/I112859197"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":5.5019,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.92788253,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"307","last_page":"316"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9884999990463257,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8305951356887817},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3375781178474426}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8305951356887817},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3375781178474426}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/978-3-031-89704-7_24","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-89704-7_24","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-89704-7_24.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:pubblicazioni.unicam.it:11581/491965","is_oa":true,"landing_page_url":"https://link.springer.com/chapter/10.1007/978-3-031-89704-7_24","pdf_url":null,"source":{"id":"https://openalex.org/S4306400819","display_name":"Unicam Scientific Publications (University of Camerino)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I112859197","host_organization_name":"Universit\u00e0 di Camerino","host_organization_lineage":["https://openalex.org/I112859197"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/bookPart"}],"best_oa_location":{"id":"doi:10.1007/978-3-031-89704-7_24","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-031-89704-7_24","pdf_url":"https://link.springer.com/content/pdf/10.1007/978-3-031-89704-7_24.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311030","display_name":"Istituto Nazionale di Alta Matematica \"Francesco Severi\"","ror":"https://ror.org/01vx64p53"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334079","display_name":"Gruppo Nazionale per il Calcolo Scientifico","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410372430.pdf","grobid_xml":"https://content.openalex.org/works/W4410372430.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1837794086","https://openalex.org/W1980722147","https://openalex.org/W1982680051","https://openalex.org/W1994042976","https://openalex.org/W2009818318","https://openalex.org/W2015292449","https://openalex.org/W2088528526","https://openalex.org/W2091705944","https://openalex.org/W2103848900","https://openalex.org/W2128356721","https://openalex.org/W2134861301","https://openalex.org/W2136480416","https://openalex.org/W2138007734","https://openalex.org/W2157483415","https://openalex.org/W2165724176","https://openalex.org/W2332111000","https://openalex.org/W2768515163","https://openalex.org/W2795006969","https://openalex.org/W2922468360","https://openalex.org/W2938347885","https://openalex.org/W3010180247","https://openalex.org/W3083127971","https://openalex.org/W3112868348","https://openalex.org/W3213133098","https://openalex.org/W4232859119","https://openalex.org/W4312469070","https://openalex.org/W6631688033"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Abstract":[0],"RNAs":[1],"are":[2,32],"single-stranded":[3],"molecules":[4],"that":[5,94],"fold":[6],"into":[7,28,123],"themselves,":[8],"determining":[9],"a":[10,35,55,80,92,151,157,168,175,195,206],"complex":[11],"shape":[12],"to":[13,135],"perform":[14],"their":[15],"biological":[16,43,60],"functions.":[17],"Considering":[18],"the":[19,63,75,96,117,145,185,199],"chemical":[20],"bonds":[21],"established,":[22],"such":[23,48],"shapes":[24],"can":[25],"be":[26],"abstracted":[27],"secondary":[29,67,99,121,192],"structures,":[30,49],"which":[31],"tractable":[33],"from":[34],"computational":[36],"point":[37],"of":[38,47,98,119,144,187,190],"view":[39],"and":[40,52,111,130,142,155],"encode":[41],"valuable":[42],"information.":[44],"The":[45,160,181],"analysis":[46],"including":[50,102],"comparison":[51],"classification,":[53],"plays":[54],"fundamental":[56],"role":[57],"in":[58,83,163,194],"different":[59,72,78],"studies.":[61],"Unfortunately,":[62],"available":[64,166],"tools":[65],"take":[66],"structures":[68,122,193],"as":[69,150,156,167,174],"input":[70],"using":[71],"formats,":[73,101],"making":[74],"translation":[76,97],"among":[77],"them":[79],"necessary":[81],"step":[82],"every":[84],"analysis.":[85],"In":[86],"this":[87],"work,":[88],"we":[89],"propose":[90],"TARNAS,":[91],"software":[93],"permits":[95,134],"structure":[100],"BPSEQ,":[103],"CT,":[104],"Dot-Bracket,":[105],"RNAML,":[106],"FASTA":[107],"(only":[108],"primary":[109],"structure)":[110],"Arc-annotated":[112],"Sequence.":[113],"TARNAS":[114,133,147],"also":[115],"allows":[116,184],"abstraction":[118],"RNA":[120,191],"three":[124],"views,":[125],"namely":[126],"Core,":[127],"Core":[128],"Plus":[129],"Shape.":[131],"Finally,":[132],"delete":[136],"or":[137,173],"retain":[138],"comments,":[139],"blank":[140],"lines":[141],"headers":[143],"files.":[146],"is":[148,165],"developed":[149,162],"standalone":[152,169,182],"desktop":[153],"application":[154,170,177],"web":[158,176,200],"app.":[159],"tool,":[161],"Java,":[164],"at":[171,178,205],"https://github.com/bdslab/TARNAS":[172],"https://bdslab.unicam.it/tarnas/":[179],".":[180],"version":[183,201],"processing":[186],"large":[188],"sets":[189],"batch":[196],"fashion,":[197],"whereas":[198],"translates":[202],"one":[203],"molecule":[204],"time.":[207]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
